Starting phenix.real_space_refine on Thu Feb 5 09:45:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pq2_71781/02_2026/9pq2_71781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pq2_71781/02_2026/9pq2_71781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pq2_71781/02_2026/9pq2_71781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pq2_71781/02_2026/9pq2_71781.map" model { file = "/net/cci-nas-00/data/ceres_data/9pq2_71781/02_2026/9pq2_71781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pq2_71781/02_2026/9pq2_71781.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10020 2.51 5 N 2544 2.21 5 O 3501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16167 Number of models: 1 Model: "" Number of chains: 60 Chain: "C" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3655 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 22, 'TRANS': 438} Chain breaks: 1 Chain: "A" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3655 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 22, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "I" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3655 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 22, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.83, per 1000 atoms: 0.24 Number of scatterers: 16167 At special positions: 0 Unit cell: (125.4, 136.125, 126.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3501 8.00 N 2544 7.00 C 10020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.13 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS F 605 " distance=1.92 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN L 4 " - " MAN L 5 " " MAN c 4 " - " MAN c 5 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA c 3 " - " MAN c 4 " " BMA e 3 " - " MAN e 4 " " BMA h 3 " - " MAN h 4 " " BMA p 3 " - " MAN p 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA L 3 " - " MAN L 6 " " BMA Q 3 " - " MAN Q 5 " " BMA Y 3 " - " MAN Y 5 " " BMA c 3 " - " MAN c 6 " " BMA h 3 " - " MAN h 5 " " BMA p 3 " - " MAN p 5 " " BMA t 3 " - " MAN t 6 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN I 130 " " NAG 1 1 " - " ASN I 160 " " NAG 2 1 " - " ASN I 230 " " NAG 3 1 " - " ASN I 392 " " NAG 4 1 " - " ASN I 442 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG D 1 " - " ASN C 133 " " NAG E 1 " - " ASN C 156 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG H 1 " - " ASN C 197 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 339 " " NAG I 603 " - " ASN I 355 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 241 " " NAG L 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 276 " " NAG N 1 " - " ASN C 289 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 130 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 230 " " NAG V 1 " - " ASN C 392 " " NAG W 1 " - " ASN C 442 " " NAG X 1 " - " ASN G 133 " " NAG Y 1 " - " ASN G 156 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 241 " " NAG c 1 " - " ASN G 262 " " NAG d 1 " - " ASN G 276 " " NAG e 1 " - " ASN G 289 " " NAG f 1 " - " ASN G 301 " " NAG g 1 " - " ASN G 332 " " NAG h 1 " - " ASN G 386 " " NAG i 1 " - " ASN G 448 " " NAG j 1 " - " ASN G 130 " " NAG k 1 " - " ASN G 160 " " NAG l 1 " - " ASN G 230 " " NAG m 1 " - " ASN G 392 " " NAG n 1 " - " ASN G 442 " " NAG o 1 " - " ASN I 133 " " NAG p 1 " - " ASN I 156 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 234 " " NAG s 1 " - " ASN I 241 " " NAG t 1 " - " ASN I 262 " " NAG u 1 " - " ASN I 276 " " NAG v 1 " - " ASN I 289 " " NAG w 1 " - " ASN I 301 " " NAG x 1 " - " ASN I 332 " " NAG y 1 " - " ASN I 386 " " NAG z 1 " - " ASN I 448 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 569.8 milliseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 25.8% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.430A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.647A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 544 removed outlier: 3.984A pdb=" N GLN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.558A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.640A pdb=" N ILE A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.573A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.429A pdb=" N ASP G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 427 through 430 Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.647A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.985A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.557A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.639A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.573A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.430A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 427 through 430 Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.646A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 544 removed outlier: 3.984A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.558A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.640A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.573A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 495 through 499 removed outlier: 3.775A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.247A pdb=" N VAL C 44 " --> pdb=" O LYS C 492 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 200 through 203 removed outlier: 7.510A pdb=" N THR C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N TYR C 435 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.513A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.511A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.600A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.511A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.833A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR C 303 " --> pdb=" O ASN C 321 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 495 through 499 removed outlier: 3.902A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 44 through 47 removed outlier: 4.247A pdb=" N VAL G 44 " --> pdb=" O LYS G 492 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'G' and resid 200 through 203 removed outlier: 7.510A pdb=" N THR G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N TYR G 435 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.512A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.511A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 333 " --> pdb=" O ILE G 414 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 273 removed outlier: 10.600A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 11.511A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE G 468 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 301 through 312 removed outlier: 6.833A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR G 303 " --> pdb=" O ASN G 321 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 495 through 499 removed outlier: 5.361A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 44 through 47 removed outlier: 4.248A pdb=" N VAL I 44 " --> pdb=" O LYS I 492 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'I' and resid 200 through 203 removed outlier: 7.510A pdb=" N THR I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N TYR I 435 " --> pdb=" O THR I 200 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.513A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 333 " --> pdb=" O ILE I 414 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 273 removed outlier: 10.600A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N PHE I 468 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 301 through 312 removed outlier: 6.833A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR I 303 " --> pdb=" O ASN I 321 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4718 1.34 - 1.47: 4437 1.47 - 1.59: 7168 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 16461 Sorted by residual: bond pdb=" C LYS G 117 " pdb=" N PRO G 118 " ideal model delta sigma weight residual 1.336 1.371 -0.035 1.20e-02 6.94e+03 8.56e+00 bond pdb=" C LYS I 117 " pdb=" N PRO I 118 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.20e-02 6.94e+03 8.15e+00 bond pdb=" C LYS C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.20e-02 6.94e+03 7.94e+00 bond pdb=" N GLU B 657 " pdb=" CA GLU B 657 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.20e-02 6.94e+03 5.63e+00 bond pdb=" N GLU F 657 " pdb=" CA GLU F 657 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.20e-02 6.94e+03 5.59e+00 ... (remaining 16456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 21817 2.51 - 5.02: 468 5.02 - 7.53: 71 7.53 - 10.03: 15 10.03 - 12.54: 9 Bond angle restraints: 22380 Sorted by residual: angle pdb=" N GLU F 657 " pdb=" CA GLU F 657 " pdb=" C GLU F 657 " ideal model delta sigma weight residual 111.14 106.31 4.83 1.08e+00 8.57e-01 2.00e+01 angle pdb=" N GLU A 657 " pdb=" CA GLU A 657 " pdb=" C GLU A 657 " ideal model delta sigma weight residual 111.14 106.34 4.80 1.08e+00 8.57e-01 1.97e+01 angle pdb=" N GLU B 657 " pdb=" CA GLU B 657 " pdb=" C GLU B 657 " ideal model delta sigma weight residual 111.14 106.35 4.79 1.08e+00 8.57e-01 1.97e+01 angle pdb=" C2 NAG i 1 " pdb=" N2 NAG i 1 " pdb=" C7 NAG i 1 " ideal model delta sigma weight residual 124.56 137.10 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C2 NAG R 1 " pdb=" N2 NAG R 1 " pdb=" C7 NAG R 1 " ideal model delta sigma weight residual 124.56 137.06 -12.50 3.00e+00 1.11e-01 1.74e+01 ... (remaining 22375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10955 17.93 - 35.85: 809 35.85 - 53.78: 215 53.78 - 71.70: 72 71.70 - 89.63: 15 Dihedral angle restraints: 12066 sinusoidal: 6966 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS I 501 " pdb=" SG CYS I 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 129.25 -36.25 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS A 605 " pdb=" CB CYS A 605 " ideal model delta sinusoidal sigma weight residual 93.00 129.18 -36.18 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -50.34 -35.66 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 12063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2558 0.066 - 0.133: 438 0.133 - 0.199: 43 0.199 - 0.265: 3 0.265 - 0.332: 9 Chirality restraints: 3051 Sorted by residual: chirality pdb=" C2 NAG X 1 " pdb=" C1 NAG X 1 " pdb=" C3 NAG X 1 " pdb=" N2 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C2 NAG o 1 " pdb=" C1 NAG o 1 " pdb=" C3 NAG o 1 " pdb=" N2 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3048 not shown) Planarity restraints: 2655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 232 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C THR I 232 " -0.044 2.00e-02 2.50e+03 pdb=" O THR I 232 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE I 233 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 232 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C THR C 232 " -0.043 2.00e-02 2.50e+03 pdb=" O THR C 232 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE C 233 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 232 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C THR G 232 " -0.043 2.00e-02 2.50e+03 pdb=" O THR G 232 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE G 233 " 0.015 2.00e-02 2.50e+03 ... (remaining 2652 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 7513 2.96 - 3.44: 14790 3.44 - 3.93: 26660 3.93 - 4.41: 27897 4.41 - 4.90: 47522 Nonbonded interactions: 124382 Sorted by model distance: nonbonded pdb=" O5 BMA t 3 " pdb=" O6 BMA t 3 " model vdw 2.472 2.432 nonbonded pdb=" O5 BMA L 3 " pdb=" O6 BMA L 3 " model vdw 2.472 2.432 nonbonded pdb=" O5 BMA c 3 " pdb=" O6 BMA c 3 " model vdw 2.473 2.432 nonbonded pdb=" O5 BMA Y 3 " pdb=" O6 BMA Y 3 " model vdw 2.516 2.432 nonbonded pdb=" O5 BMA p 3 " pdb=" O6 BMA p 3 " model vdw 2.516 2.432 ... (remaining 124377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '4' selection = chain 'D' selection = chain 'O' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'f' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'w' } ncs_group { reference = chain '1' selection = chain '2' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'Y' selection = chain 'h' selection = chain 'p' selection = chain 'y' } ncs_group { reference = chain 'L' selection = chain 'c' selection = chain 't' } ncs_group { reference = chain 'N' selection = chain 'e' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 16665 Z= 0.207 Angle : 0.936 12.543 22959 Z= 0.457 Chirality : 0.052 0.332 3051 Planarity : 0.005 0.052 2595 Dihedral : 13.249 89.625 8667 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.15 % Allowed : 17.59 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1734 helix: -0.12 (0.23), residues: 432 sheet: -0.67 (0.23), residues: 477 loop : -0.39 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 46 TYR 0.008 0.001 TYR I 395 PHE 0.011 0.001 PHE G 223 TRP 0.024 0.002 TRP A 571 HIS 0.006 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00403 (16461) covalent geometry : angle 0.90581 (22380) SS BOND : bond 0.02634 ( 33) SS BOND : angle 1.33063 ( 66) hydrogen bonds : bond 0.14622 ( 538) hydrogen bonds : angle 6.52962 ( 1542) link_ALPHA1-2 : bond 0.01006 ( 3) link_ALPHA1-2 : angle 1.68257 ( 9) link_ALPHA1-3 : bond 0.01074 ( 12) link_ALPHA1-3 : angle 1.44966 ( 36) link_ALPHA1-6 : bond 0.00467 ( 9) link_ALPHA1-6 : angle 1.37037 ( 27) link_BETA1-4 : bond 0.00680 ( 87) link_BETA1-4 : angle 1.77573 ( 261) link_NAG-ASN : bond 0.00229 ( 60) link_NAG-ASN : angle 1.91385 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8823 (tpp) cc_final: 0.8498 (mmm) REVERT: A 543 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 619 GLU cc_start: 0.8721 (tt0) cc_final: 0.8250 (tm-30) REVERT: A 626 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7756 (tpt) REVERT: A 644 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8478 (ptp90) REVERT: A 653 GLN cc_start: 0.8683 (tt0) cc_final: 0.8100 (mt0) REVERT: B 530 MET cc_start: 0.8394 (mmt) cc_final: 0.7961 (mmm) REVERT: B 543 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 570 VAL cc_start: 0.8996 (t) cc_final: 0.8713 (p) REVERT: B 626 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7385 (tpt) REVERT: B 644 ARG cc_start: 0.8608 (mtm110) cc_final: 0.8271 (mtm-85) REVERT: B 653 GLN cc_start: 0.8786 (tt0) cc_final: 0.8339 (tm-30) REVERT: F 522 PHE cc_start: 0.8343 (t80) cc_final: 0.8035 (t80) REVERT: F 543 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8288 (tm-30) REVERT: F 584 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8717 (mt-10) REVERT: F 619 GLU cc_start: 0.8831 (tt0) cc_final: 0.8240 (tm-30) REVERT: F 635 ILE cc_start: 0.9070 (mm) cc_final: 0.8818 (mp) REVERT: F 644 ARG cc_start: 0.8630 (mtm110) cc_final: 0.8206 (ptp90) outliers start: 18 outliers final: 13 residues processed: 213 average time/residue: 0.1387 time to fit residues: 42.1164 Evaluate side-chains 185 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 604 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 328 GLN C 340 ASN A 540 GLN A 636 ASN B 636 ASN ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN F 636 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.078023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.059322 restraints weight = 48688.559| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.36 r_work: 0.2818 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16665 Z= 0.218 Angle : 0.688 9.862 22959 Z= 0.313 Chirality : 0.045 0.262 3051 Planarity : 0.004 0.034 2595 Dihedral : 7.083 58.899 5375 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.08 % Allowed : 14.21 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1734 helix: 1.21 (0.26), residues: 417 sheet: -0.48 (0.24), residues: 441 loop : -0.32 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 46 TYR 0.010 0.001 TYR I 177 PHE 0.010 0.001 PHE I 223 TRP 0.014 0.002 TRP G 112 HIS 0.004 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00491 (16461) covalent geometry : angle 0.64252 (22380) SS BOND : bond 0.00384 ( 33) SS BOND : angle 1.02865 ( 66) hydrogen bonds : bond 0.03833 ( 538) hydrogen bonds : angle 4.76729 ( 1542) link_ALPHA1-2 : bond 0.00598 ( 3) link_ALPHA1-2 : angle 1.34397 ( 9) link_ALPHA1-3 : bond 0.00666 ( 12) link_ALPHA1-3 : angle 1.43690 ( 36) link_ALPHA1-6 : bond 0.00377 ( 9) link_ALPHA1-6 : angle 1.52837 ( 27) link_BETA1-4 : bond 0.00433 ( 87) link_BETA1-4 : angle 1.77089 ( 261) link_NAG-ASN : bond 0.00355 ( 60) link_NAG-ASN : angle 1.81584 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: C 303 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9025 (p) REVERT: C 427 TRP cc_start: 0.8371 (m-10) cc_final: 0.8073 (m-10) REVERT: A 543 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 626 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8212 (ttt) REVERT: A 633 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8602 (mmm160) REVERT: A 644 ARG cc_start: 0.8908 (mtm110) cc_final: 0.8472 (ptp90) REVERT: A 653 GLN cc_start: 0.8900 (tt0) cc_final: 0.8452 (mt0) REVERT: G 114 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8909 (mt0) REVERT: G 303 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9082 (p) REVERT: G 427 TRP cc_start: 0.8393 (m-10) cc_final: 0.8160 (m-10) REVERT: B 543 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 653 GLN cc_start: 0.8883 (tt0) cc_final: 0.8459 (tm-30) REVERT: I 154 MET cc_start: 0.9085 (mtp) cc_final: 0.8501 (mtp) REVERT: I 303 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8878 (p) REVERT: F 543 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8139 (tm-30) REVERT: F 584 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8777 (mt-10) REVERT: F 619 GLU cc_start: 0.8909 (tt0) cc_final: 0.8251 (tm-30) REVERT: F 644 ARG cc_start: 0.8697 (mtm110) cc_final: 0.8368 (ptp90) outliers start: 64 outliers final: 21 residues processed: 233 average time/residue: 0.1336 time to fit residues: 45.3853 Evaluate side-chains 187 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 636 ASN B 540 GLN B 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.056216 restraints weight = 48454.842| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.51 r_work: 0.2790 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16665 Z= 0.190 Angle : 0.658 9.521 22959 Z= 0.298 Chirality : 0.045 0.261 3051 Planarity : 0.003 0.048 2595 Dihedral : 6.850 58.732 5364 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.06 % Allowed : 16.63 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1734 helix: 1.53 (0.26), residues: 417 sheet: -0.45 (0.24), residues: 441 loop : -0.34 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 633 TYR 0.016 0.001 TYR G 399 PHE 0.010 0.001 PHE C 223 TRP 0.016 0.001 TRP G 112 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00428 (16461) covalent geometry : angle 0.61851 (22380) SS BOND : bond 0.00319 ( 33) SS BOND : angle 0.94783 ( 66) hydrogen bonds : bond 0.03629 ( 538) hydrogen bonds : angle 4.62230 ( 1542) link_ALPHA1-2 : bond 0.00724 ( 3) link_ALPHA1-2 : angle 1.41240 ( 9) link_ALPHA1-3 : bond 0.00819 ( 12) link_ALPHA1-3 : angle 1.31905 ( 36) link_ALPHA1-6 : bond 0.00400 ( 9) link_ALPHA1-6 : angle 1.51438 ( 27) link_BETA1-4 : bond 0.00469 ( 87) link_BETA1-4 : angle 1.64529 ( 261) link_NAG-ASN : bond 0.00242 ( 60) link_NAG-ASN : angle 1.64198 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: C 303 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9053 (p) REVERT: C 427 TRP cc_start: 0.8423 (m-10) cc_final: 0.8081 (m-10) REVERT: A 543 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 633 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8597 (mmm160) REVERT: A 644 ARG cc_start: 0.8941 (mtm110) cc_final: 0.8537 (ptp90) REVERT: A 653 GLN cc_start: 0.8917 (tt0) cc_final: 0.8446 (mt0) REVERT: G 303 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9060 (p) REVERT: G 427 TRP cc_start: 0.8390 (m-10) cc_final: 0.8076 (m-10) REVERT: B 543 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8005 (tm-30) REVERT: I 154 MET cc_start: 0.9080 (mtp) cc_final: 0.8558 (mtp) REVERT: I 303 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8931 (p) REVERT: F 543 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8073 (tm-30) REVERT: F 619 GLU cc_start: 0.8916 (tt0) cc_final: 0.8280 (tm-30) outliers start: 48 outliers final: 30 residues processed: 217 average time/residue: 0.1344 time to fit residues: 42.1195 Evaluate side-chains 198 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN F 540 GLN F 636 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.075844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056600 restraints weight = 47666.874| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.46 r_work: 0.2790 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16665 Z= 0.143 Angle : 0.626 9.457 22959 Z= 0.281 Chirality : 0.044 0.253 3051 Planarity : 0.003 0.028 2595 Dihedral : 6.592 57.318 5361 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.74 % Allowed : 17.78 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1734 helix: 1.75 (0.26), residues: 417 sheet: -0.45 (0.24), residues: 435 loop : -0.32 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 633 TYR 0.006 0.001 TYR C 217 PHE 0.009 0.001 PHE C 223 TRP 0.013 0.001 TRP G 112 HIS 0.010 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00319 (16461) covalent geometry : angle 0.58630 (22380) SS BOND : bond 0.00279 ( 33) SS BOND : angle 0.90461 ( 66) hydrogen bonds : bond 0.03328 ( 538) hydrogen bonds : angle 4.43743 ( 1542) link_ALPHA1-2 : bond 0.00695 ( 3) link_ALPHA1-2 : angle 1.47639 ( 9) link_ALPHA1-3 : bond 0.00802 ( 12) link_ALPHA1-3 : angle 1.31695 ( 36) link_ALPHA1-6 : bond 0.00429 ( 9) link_ALPHA1-6 : angle 1.46651 ( 27) link_BETA1-4 : bond 0.00442 ( 87) link_BETA1-4 : angle 1.61283 ( 261) link_NAG-ASN : bond 0.00188 ( 60) link_NAG-ASN : angle 1.54354 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: C 303 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9077 (p) REVERT: C 427 TRP cc_start: 0.8414 (m-10) cc_final: 0.8085 (m-10) REVERT: A 543 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 626 MET cc_start: 0.8758 (tpt) cc_final: 0.8492 (tpt) REVERT: A 653 GLN cc_start: 0.8910 (tt0) cc_final: 0.8446 (mt0) REVERT: G 114 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8918 (mt0) REVERT: G 303 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9060 (p) REVERT: G 427 TRP cc_start: 0.8393 (m-10) cc_final: 0.8128 (m-10) REVERT: B 543 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 584 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8929 (mt-10) REVERT: I 303 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8950 (p) REVERT: I 427 TRP cc_start: 0.8511 (m-10) cc_final: 0.8181 (m-10) REVERT: F 543 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8123 (tm-30) REVERT: F 619 GLU cc_start: 0.8861 (tt0) cc_final: 0.8258 (tm-30) outliers start: 43 outliers final: 26 residues processed: 212 average time/residue: 0.1424 time to fit residues: 44.1093 Evaluate side-chains 195 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 139 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN B 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.076331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057138 restraints weight = 47733.935| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.43 r_work: 0.2815 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16665 Z= 0.121 Angle : 0.609 9.483 22959 Z= 0.273 Chirality : 0.044 0.252 3051 Planarity : 0.003 0.028 2595 Dihedral : 6.402 56.718 5358 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.74 % Allowed : 18.36 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1734 helix: 1.99 (0.26), residues: 414 sheet: -0.43 (0.24), residues: 435 loop : -0.21 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 633 TYR 0.014 0.001 TYR G 399 PHE 0.009 0.001 PHE C 223 TRP 0.013 0.001 TRP G 112 HIS 0.004 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00265 (16461) covalent geometry : angle 0.57127 (22380) SS BOND : bond 0.00361 ( 33) SS BOND : angle 0.71647 ( 66) hydrogen bonds : bond 0.03146 ( 538) hydrogen bonds : angle 4.30939 ( 1542) link_ALPHA1-2 : bond 0.00737 ( 3) link_ALPHA1-2 : angle 1.47595 ( 9) link_ALPHA1-3 : bond 0.00817 ( 12) link_ALPHA1-3 : angle 1.31749 ( 36) link_ALPHA1-6 : bond 0.00463 ( 9) link_ALPHA1-6 : angle 1.44330 ( 27) link_BETA1-4 : bond 0.00454 ( 87) link_BETA1-4 : angle 1.57972 ( 261) link_NAG-ASN : bond 0.00151 ( 60) link_NAG-ASN : angle 1.46673 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: C 303 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9055 (p) REVERT: C 427 TRP cc_start: 0.8382 (m-10) cc_final: 0.8082 (m-10) REVERT: A 542 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8572 (mmm-85) REVERT: A 543 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 633 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8655 (mmm160) REVERT: A 644 ARG cc_start: 0.8940 (mtm110) cc_final: 0.8582 (ptp90) REVERT: G 114 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8889 (mt0) REVERT: G 303 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9036 (p) REVERT: G 427 TRP cc_start: 0.8363 (m-10) cc_final: 0.8117 (m-10) REVERT: B 530 MET cc_start: 0.8654 (mmm) cc_final: 0.8189 (mtp) REVERT: B 543 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8164 (tm-30) REVERT: I 303 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8951 (p) REVERT: I 427 TRP cc_start: 0.8493 (m-10) cc_final: 0.8235 (m-10) REVERT: I 475 MET cc_start: 0.9260 (mmm) cc_final: 0.8896 (tpt) REVERT: F 543 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8093 (tm-30) REVERT: F 584 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8850 (mt-10) REVERT: F 619 GLU cc_start: 0.8842 (tt0) cc_final: 0.8192 (tm-30) outliers start: 43 outliers final: 25 residues processed: 213 average time/residue: 0.1419 time to fit residues: 44.3384 Evaluate side-chains 193 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 ASN A 540 GLN B 540 GLN I 151 ASN F 540 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.075752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.056482 restraints weight = 47661.592| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.45 r_work: 0.2786 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16665 Z= 0.147 Angle : 0.620 9.597 22959 Z= 0.278 Chirality : 0.044 0.275 3051 Planarity : 0.003 0.035 2595 Dihedral : 6.396 57.106 5358 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.31 % Allowed : 18.67 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1734 helix: 2.05 (0.26), residues: 414 sheet: -0.42 (0.24), residues: 429 loop : -0.22 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 46 TYR 0.006 0.001 TYR I 401 PHE 0.010 0.001 PHE C 223 TRP 0.013 0.001 TRP G 112 HIS 0.002 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00331 (16461) covalent geometry : angle 0.58145 (22380) SS BOND : bond 0.00263 ( 33) SS BOND : angle 0.75968 ( 66) hydrogen bonds : bond 0.03176 ( 538) hydrogen bonds : angle 4.29025 ( 1542) link_ALPHA1-2 : bond 0.00711 ( 3) link_ALPHA1-2 : angle 1.41652 ( 9) link_ALPHA1-3 : bond 0.00773 ( 12) link_ALPHA1-3 : angle 1.33425 ( 36) link_ALPHA1-6 : bond 0.00439 ( 9) link_ALPHA1-6 : angle 1.45814 ( 27) link_BETA1-4 : bond 0.00443 ( 87) link_BETA1-4 : angle 1.59687 ( 261) link_NAG-ASN : bond 0.00194 ( 60) link_NAG-ASN : angle 1.51101 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 427 TRP cc_start: 0.8418 (m-10) cc_final: 0.8086 (m-10) REVERT: A 542 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8674 (mmm-85) REVERT: A 543 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 633 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8642 (mmm160) REVERT: G 303 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9058 (p) REVERT: G 427 TRP cc_start: 0.8373 (m-10) cc_final: 0.8122 (m-10) REVERT: B 530 MET cc_start: 0.8747 (mmm) cc_final: 0.8339 (mtp) REVERT: B 543 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8227 (tm-30) REVERT: I 303 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8999 (p) REVERT: I 427 TRP cc_start: 0.8519 (m-10) cc_final: 0.8243 (m-10) REVERT: F 543 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8164 (tm-30) REVERT: F 584 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8828 (mt-10) REVERT: F 619 GLU cc_start: 0.8871 (tt0) cc_final: 0.8137 (tm-30) outliers start: 52 outliers final: 31 residues processed: 215 average time/residue: 0.1420 time to fit residues: 44.8727 Evaluate side-chains 201 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN G 67 ASN G 151 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.075606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054358 restraints weight = 49812.214| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.77 r_work: 0.2730 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16665 Z= 0.168 Angle : 0.637 9.465 22959 Z= 0.288 Chirality : 0.044 0.260 3051 Planarity : 0.003 0.036 2595 Dihedral : 6.447 57.443 5358 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.06 % Allowed : 18.99 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1734 helix: 2.07 (0.26), residues: 414 sheet: -0.40 (0.24), residues: 435 loop : -0.14 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 633 TYR 0.016 0.001 TYR G 399 PHE 0.009 0.001 PHE C 223 TRP 0.013 0.001 TRP G 112 HIS 0.003 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00380 (16461) covalent geometry : angle 0.59897 (22380) SS BOND : bond 0.00299 ( 33) SS BOND : angle 0.85038 ( 66) hydrogen bonds : bond 0.03311 ( 538) hydrogen bonds : angle 4.34342 ( 1542) link_ALPHA1-2 : bond 0.00687 ( 3) link_ALPHA1-2 : angle 1.39097 ( 9) link_ALPHA1-3 : bond 0.00707 ( 12) link_ALPHA1-3 : angle 1.33070 ( 36) link_ALPHA1-6 : bond 0.00425 ( 9) link_ALPHA1-6 : angle 1.46487 ( 27) link_BETA1-4 : bond 0.00433 ( 87) link_BETA1-4 : angle 1.60730 ( 261) link_NAG-ASN : bond 0.00250 ( 60) link_NAG-ASN : angle 1.56349 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: C 427 TRP cc_start: 0.8409 (m-10) cc_final: 0.7982 (m-10) REVERT: A 530 MET cc_start: 0.8874 (mmm) cc_final: 0.8409 (mtp) REVERT: A 542 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8572 (mmm-85) REVERT: A 543 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8259 (tm-30) REVERT: A 626 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8284 (ttt) REVERT: A 633 ARG cc_start: 0.9030 (mmm160) cc_final: 0.8722 (mmm160) REVERT: G 303 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8918 (p) REVERT: G 427 TRP cc_start: 0.8432 (m-10) cc_final: 0.8092 (m-10) REVERT: B 530 MET cc_start: 0.8775 (mmm) cc_final: 0.8441 (mtp) REVERT: B 543 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8109 (tm-30) REVERT: I 303 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8899 (p) REVERT: I 427 TRP cc_start: 0.8566 (m-10) cc_final: 0.8173 (m-10) REVERT: F 543 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8129 (tm-30) REVERT: F 619 GLU cc_start: 0.8827 (tt0) cc_final: 0.8046 (tm-30) outliers start: 48 outliers final: 35 residues processed: 211 average time/residue: 0.1445 time to fit residues: 44.7754 Evaluate side-chains 203 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.075602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054406 restraints weight = 50164.010| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.78 r_work: 0.2736 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16665 Z= 0.154 Angle : 0.637 9.474 22959 Z= 0.289 Chirality : 0.044 0.264 3051 Planarity : 0.003 0.043 2595 Dihedral : 6.416 57.166 5358 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.25 % Allowed : 19.18 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1734 helix: 2.08 (0.26), residues: 414 sheet: -0.41 (0.24), residues: 435 loop : -0.12 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 633 TYR 0.007 0.001 TYR I 401 PHE 0.009 0.001 PHE C 223 TRP 0.013 0.001 TRP G 112 HIS 0.004 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00350 (16461) covalent geometry : angle 0.60058 (22380) SS BOND : bond 0.00276 ( 33) SS BOND : angle 0.83384 ( 66) hydrogen bonds : bond 0.03236 ( 538) hydrogen bonds : angle 4.32298 ( 1542) link_ALPHA1-2 : bond 0.00702 ( 3) link_ALPHA1-2 : angle 1.41619 ( 9) link_ALPHA1-3 : bond 0.00732 ( 12) link_ALPHA1-3 : angle 1.32662 ( 36) link_ALPHA1-6 : bond 0.00448 ( 9) link_ALPHA1-6 : angle 1.45701 ( 27) link_BETA1-4 : bond 0.00436 ( 87) link_BETA1-4 : angle 1.58848 ( 261) link_NAG-ASN : bond 0.00212 ( 60) link_NAG-ASN : angle 1.50973 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 427 TRP cc_start: 0.8422 (m-10) cc_final: 0.8034 (m-10) REVERT: A 530 MET cc_start: 0.8881 (mmm) cc_final: 0.8421 (mtp) REVERT: A 542 ARG cc_start: 0.8935 (mmm-85) cc_final: 0.8595 (mmm-85) REVERT: A 543 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 626 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8292 (ttt) REVERT: A 633 ARG cc_start: 0.9051 (mmm160) cc_final: 0.8737 (mmm160) REVERT: G 303 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8868 (p) REVERT: G 427 TRP cc_start: 0.8466 (m-10) cc_final: 0.8120 (m-10) REVERT: B 530 MET cc_start: 0.8785 (mmm) cc_final: 0.8323 (mtp) REVERT: B 543 GLN cc_start: 0.8627 (tm-30) cc_final: 0.7997 (tm-30) REVERT: I 154 MET cc_start: 0.9119 (mtm) cc_final: 0.8811 (mtp) REVERT: I 303 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8902 (p) REVERT: I 427 TRP cc_start: 0.8580 (m-10) cc_final: 0.8186 (m-10) REVERT: I 475 MET cc_start: 0.9217 (tpp) cc_final: 0.8907 (tpt) REVERT: F 543 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8165 (tm-30) REVERT: F 619 GLU cc_start: 0.8813 (tt0) cc_final: 0.8038 (tm-30) REVERT: F 626 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (ttt) outliers start: 51 outliers final: 39 residues processed: 212 average time/residue: 0.1375 time to fit residues: 42.7275 Evaluate side-chains 209 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN G 67 ASN B 636 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054785 restraints weight = 49918.445| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.80 r_work: 0.2740 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16665 Z= 0.139 Angle : 0.629 9.482 22959 Z= 0.286 Chirality : 0.044 0.261 3051 Planarity : 0.003 0.040 2595 Dihedral : 6.343 56.951 5358 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.80 % Allowed : 19.63 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1734 helix: 2.13 (0.26), residues: 414 sheet: -0.41 (0.24), residues: 435 loop : -0.11 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 633 TYR 0.014 0.001 TYR G 399 PHE 0.008 0.001 PHE I 223 TRP 0.013 0.001 TRP A 571 HIS 0.003 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00313 (16461) covalent geometry : angle 0.59311 (22380) SS BOND : bond 0.00284 ( 33) SS BOND : angle 0.77218 ( 66) hydrogen bonds : bond 0.03140 ( 538) hydrogen bonds : angle 4.27772 ( 1542) link_ALPHA1-2 : bond 0.00714 ( 3) link_ALPHA1-2 : angle 1.42998 ( 9) link_ALPHA1-3 : bond 0.00711 ( 12) link_ALPHA1-3 : angle 1.31893 ( 36) link_ALPHA1-6 : bond 0.00468 ( 9) link_ALPHA1-6 : angle 1.44661 ( 27) link_BETA1-4 : bond 0.00439 ( 87) link_BETA1-4 : angle 1.57210 ( 261) link_NAG-ASN : bond 0.00186 ( 60) link_NAG-ASN : angle 1.46401 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 427 TRP cc_start: 0.8433 (m-10) cc_final: 0.8064 (m-10) REVERT: A 543 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 626 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: G 303 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8856 (p) REVERT: G 427 TRP cc_start: 0.8466 (m-10) cc_final: 0.8087 (m-10) REVERT: B 530 MET cc_start: 0.8802 (mmm) cc_final: 0.8474 (mtp) REVERT: B 543 GLN cc_start: 0.8653 (tm-30) cc_final: 0.7998 (tm-30) REVERT: I 154 MET cc_start: 0.9130 (mtm) cc_final: 0.8806 (mtp) REVERT: I 303 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8818 (p) REVERT: I 427 TRP cc_start: 0.8569 (m-10) cc_final: 0.8133 (m-10) REVERT: F 543 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8188 (tm-30) REVERT: F 584 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8805 (mt-10) REVERT: F 619 GLU cc_start: 0.8813 (tt0) cc_final: 0.8060 (tm-30) REVERT: F 644 ARG cc_start: 0.8788 (mtm110) cc_final: 0.8290 (mtm-85) outliers start: 44 outliers final: 35 residues processed: 209 average time/residue: 0.1488 time to fit residues: 45.5623 Evaluate side-chains 206 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.077784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.057016 restraints weight = 50501.940| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.68 r_work: 0.2756 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16665 Z= 0.125 Angle : 0.631 9.503 22959 Z= 0.287 Chirality : 0.044 0.258 3051 Planarity : 0.003 0.047 2595 Dihedral : 6.271 56.730 5358 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.80 % Allowed : 19.38 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1734 helix: 2.18 (0.26), residues: 414 sheet: -0.42 (0.24), residues: 435 loop : -0.10 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 46 TYR 0.005 0.001 TYR A 586 PHE 0.008 0.001 PHE G 223 TRP 0.013 0.001 TRP G 112 HIS 0.002 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00278 (16461) covalent geometry : angle 0.59719 (22380) SS BOND : bond 0.00276 ( 33) SS BOND : angle 0.67336 ( 66) hydrogen bonds : bond 0.03053 ( 538) hydrogen bonds : angle 4.23012 ( 1542) link_ALPHA1-2 : bond 0.00724 ( 3) link_ALPHA1-2 : angle 1.44846 ( 9) link_ALPHA1-3 : bond 0.00719 ( 12) link_ALPHA1-3 : angle 1.31943 ( 36) link_ALPHA1-6 : bond 0.00484 ( 9) link_ALPHA1-6 : angle 1.43172 ( 27) link_BETA1-4 : bond 0.00444 ( 87) link_BETA1-4 : angle 1.55904 ( 261) link_NAG-ASN : bond 0.00158 ( 60) link_NAG-ASN : angle 1.40541 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 TRP cc_start: 0.8416 (m-10) cc_final: 0.8061 (m-10) REVERT: A 543 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 584 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8798 (mt-10) REVERT: A 626 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8365 (ttt) REVERT: A 633 ARG cc_start: 0.9031 (mmm160) cc_final: 0.8784 (mmm160) REVERT: G 303 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8847 (p) REVERT: G 427 TRP cc_start: 0.8461 (m-10) cc_final: 0.8096 (m-10) REVERT: B 530 MET cc_start: 0.8791 (mmm) cc_final: 0.8432 (mtp) REVERT: B 543 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 630 GLN cc_start: 0.9080 (mt0) cc_final: 0.8730 (mp10) REVERT: I 303 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8746 (p) REVERT: I 427 TRP cc_start: 0.8579 (m-10) cc_final: 0.8147 (m-10) REVERT: F 543 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8182 (tm-30) REVERT: F 584 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8806 (mt-10) REVERT: F 619 GLU cc_start: 0.8802 (tt0) cc_final: 0.8024 (tm-30) REVERT: F 644 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8284 (mtm-85) outliers start: 44 outliers final: 32 residues processed: 209 average time/residue: 0.1274 time to fit residues: 39.6302 Evaluate side-chains 204 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain I residue 182 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 620 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 113 optimal weight: 0.7980 chunk 141 optimal weight: 0.1980 chunk 170 optimal weight: 0.7980 chunk 110 optimal weight: 0.0470 chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055612 restraints weight = 49644.092| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.78 r_work: 0.2767 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16665 Z= 0.114 Angle : 0.623 9.514 22959 Z= 0.284 Chirality : 0.044 0.255 3051 Planarity : 0.003 0.056 2595 Dihedral : 6.174 56.452 5358 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.42 % Allowed : 20.01 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1734 helix: 2.25 (0.26), residues: 414 sheet: -0.56 (0.23), residues: 489 loop : 0.02 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 46 TYR 0.013 0.001 TYR G 399 PHE 0.008 0.001 PHE I 223 TRP 0.014 0.001 TRP G 112 HIS 0.002 0.000 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00251 (16461) covalent geometry : angle 0.59013 (22380) SS BOND : bond 0.00188 ( 33) SS BOND : angle 0.67383 ( 66) hydrogen bonds : bond 0.02955 ( 538) hydrogen bonds : angle 4.16677 ( 1542) link_ALPHA1-2 : bond 0.00736 ( 3) link_ALPHA1-2 : angle 1.45905 ( 9) link_ALPHA1-3 : bond 0.00720 ( 12) link_ALPHA1-3 : angle 1.32018 ( 36) link_ALPHA1-6 : bond 0.00500 ( 9) link_ALPHA1-6 : angle 1.42022 ( 27) link_BETA1-4 : bond 0.00451 ( 87) link_BETA1-4 : angle 1.54411 ( 261) link_NAG-ASN : bond 0.00141 ( 60) link_NAG-ASN : angle 1.36003 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.71 seconds wall clock time: 65 minutes 2.65 seconds (3902.65 seconds total)